SMTL ID : 6ud5.1

Crystal structure of human tryptophan 2,3-dioxygenase in complex with carbon monoxide and tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 31 residues within 4Å: Chain A: F.56, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain B: Y.26 Ligands: CMO.2, TRP.3 29 PLIP interactions: 25 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:F.56, A:Y.63, A:Y.63, A:Y.63, A:F.67, A:F.124, A:F.137, A:F.142, A:M.319, A:L.320, A:L.335 Hydrogen bonds: A:S.135, A:N.160, A:R.309, A:T.326, A:G.327, A:G.328, A:S.329, A:S.329, A:Y.334, W.3 Water bridges: A:R.143, A:R.156 Salt bridges: A:R.143 pi-Stacking: A:H.312, W.3, W.3 Metal complexes: A:H.312, CMO.2 HEM.5: 31 residues within 4Å: Chain A: Y.26 Chain B: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Ligands: CMO.6, TRP.7 28 PLIP interactions: 3 Ligand-Ligand interactions, 25 interactions with chain B Hydrogen bonds: W.7, B:S.135, B:S.135, B:G.327, B:G.328, B:S.329, B:Y.334 pi-Stacking: W.7, B:H.312 Metal complexes: CMO.6, B:H.312 Hydrophobic interactions: B:F.56, B:T.59, B:Y.63, B:Y.63, B:Y.63, B:F.67, B:F.124, B:F.137, B:F.142, B:W.308, B:M.319, B:L.320, B:L.335 Water bridges: B:R.143, B:R.143, B:T.338 Salt bridges: B:R.143 HEM.9: 31 residues within 4Å: Chain C: F.56, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain D: Y.26 Ligands: CMO.10, TRP.11 29 PLIP interactions: 25 interactions with chain C, 4 Ligand-Ligand interactions Hydrophobic interactions: C:F.56, C:Y.63, C:Y.63, C:Y.63, C:F.67, C:F.124, C:F.137, C:F.142, C:W.308, C:M.319, C:L.320, C:L.335, C:L.335 Hydrogen bonds: C:S.135, C:S.135, C:R.309, C:G.325, C:G.327, C:G.328, C:S.329, C:Y.334, W.11 Water bridges: C:R.143, C:R.143 Salt bridges: C:R.143 Metal complexes: C:H.312, CMO.10 pi-Stacking: W.11, W.11 HEM.13: 32 residues within 4Å: Chain C: Y.26 Chain D: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Ligands: CMO.14, TRP.15 27 PLIP interactions: 25 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.56, D:T.59, D:Y.63, D:Y.63, D:Y.63, D:F.67, D:F.124, D:F.137, D:F.142, D:W.308, D:M.319, D:L.320, D:L.335 Hydrogen bonds: D:S.135, D:S.135, D:R.309, D:T.326, D:G.327, D:G.328, D:S.329, W.15 Water bridges: D:R.143, D:R.143 Salt bridges: D:R.143 pi-Stacking: D:H.312, W.15 Metal complexes: D:H.312

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 5 residues within 4Å: Chain A: S.135, G.136, H.312 Ligands: HEM.1, TRP.3 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Water bridges: W.3 Hydrogen bonds: A:G.136 CMO.6: 5 residues within 4Å: Chain B: S.135, G.136, H.312 Ligands: HEM.5, TRP.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.136 Water bridges: W.7 CMO.10: 5 residues within 4Å: Chain C: S.135, G.136, H.312 Ligands: HEM.9, TRP.11 1 PLIP interactions: 1 Ligand-Ligand interactions Water bridges: W.11 CMO.14: 4 residues within 4Å: Chain D: S.135, G.136 Ligands: HEM.13, TRP.15 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain D Water bridges: W.15 Hydrogen bonds: D:G.136

8 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 13 residues within 4Å: Chain A: F.56, H.60, F.124, R.128, L.131, A.134, L.320, G.325, T.326 Chain B: Y.26, Y.29 Ligands: HEM.1, CMO.2 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:Y.26, B:Y.26, B:Y.29, A:F.56, A:A.134 Hydrogen bonds: A:H.60, A:T.326 Water bridges: A:S.135 Salt bridges: A:R.128 pi-Stacking: A:F.56 TRP.4: 11 residues within 4Å: Chain A: V.86, R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.192, A:P.197, A:I.279, A:F.288, A:F.288, A:P.291 Hydrogen bonds: A:V.86, A:E.89, A:W.192, W.4 Water bridges: A:R.87 Salt bridges: A:R.87, A:R.195 TRP.7: 13 residues within 4Å: Chain A: Y.26, Y.29 Chain B: F.56, H.60, F.124, R.128, L.131, A.134, L.320, G.325, T.326 Ligands: HEM.5, CMO.6 13 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions, 3 interactions with chain A Hydrophobic interactions: B:F.56, B:L.131, B:L.131, B:A.134, A:Y.26, A:Y.26, A:Y.29 Hydrogen bonds: B:H.60, B:T.326, W.7, W.7 Salt bridges: B:R.128 pi-Stacking: B:F.56 TRP.8: 11 residues within 4Å: Chain B: V.86, R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:W.192, B:P.197, B:I.279, B:F.288, B:F.288, B:P.291 Hydrogen bonds: B:E.89, B:W.192 Salt bridges: B:R.87, B:R.195 TRP.11: 13 residues within 4Å: Chain C: F.56, H.60, F.124, R.128, L.131, A.134, L.320, G.325, T.326 Chain D: Y.26, Y.29 Ligands: HEM.9, CMO.10 13 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.56, C:L.131, C:L.131, C:A.134, D:Y.26, D:Y.26, D:Y.29 Hydrogen bonds: C:H.60, C:T.326, C:T.326, W.11 Salt bridges: C:R.128 pi-Stacking: C:F.56 TRP.12: 10 residues within 4Å: Chain C: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:W.192, C:P.197, C:I.279, C:F.288, C:F.288, C:P.291 Hydrogen bonds: C:E.89, C:E.89, C:W.192 Salt bridges: C:R.87, C:R.195 TRP.15: 13 residues within 4Å: Chain C: Y.26, Y.29 Chain D: F.56, H.60, F.124, R.128, L.131, A.134, L.320, G.325, T.326 Ligands: HEM.13, CMO.14 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D, Hydrophobic interactions: C:Y.26, C:Y.29, D:F.56, D:L.131, D:L.131, D:A.134 Hydrogen bonds: D:H.60, D:T.326 Salt bridges: D:R.128 pi-Stacking: D:F.56 TRP.16: 10 residues within 4Å: Chain D: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:W.192, D:P.197, D:I.279, D:F.288, D:F.288, D:P.291 Hydrogen bonds: D:R.87, D:E.89, D:W.192, W.16 Salt bridges: D:R.87, D:R.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, K.N. et al., Conformational Plasticity in Human Heme-Based Dioxygenases. J.Am.Chem.Soc. (2021)

Release Date

2021-02-03

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophan 2,3-dioxygenase

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